Let's Encrypt Verification & CodeIgniter

I've recently been experimenting with automated certificate renewals (having previously done it manually).

What I've found is that on websites not created using CI, the whole process is painless.  However, when trying to implement it on my (still under development) CI site, what worked elsewhere fails, with a couple of complaints... the most significant that the Let's Encrypt server can't get verify the secret pushed into the website's directory).

I've not spent a lot of time on it yet, but, as interaction for the Let's Encrypt cert renewal verification is all done over HTTP, as an initial hack, I have tried to disable the automatic redirection to the HTTPS version of the site (by Apache) and also the request upgrade to HTTPS in the CI setup, but that didn't appear to make much difference (yes, Apache was restarted).

I suspect there's also issues with the CI routing that may be impeding the verification step of Let's Encrypt (?).

As this is looking like it's going to become one of those multiple-day-wasting problems, I was hoping that someone with a better grip on Let's Encrypt's interaction with CI could please give me some pointers?

Thanks.